You have to enter the Form SSA-1099 on your tax return. The form is not sent with a tax return only the tax data from the form is sent.
To enter Social Security benefits reported on form SSA-1099
Or enter ssa-1099 in the Search box located in the upper right of the program screen. Click on Jump to ssa-1099
Did you enter the SSA-1099? If the IRS says some of it is taxable it is because they increased some other income like the taxable amount of any 1099R you got.
And if you reported your pension or IRA on the wrong line the IRS might miss it and say you didn't report it. I would check for those. For 2017 and prior, IRAs go on 1040 line 15 (1040A line 11) and Pensions and 401k go on 1040 line 16 (1040A line 12). And Make sure you got the right taxable amount on the “b” line.
All of your SS is not taxable. Only up to 85% of Social Security becomes taxable when all your other income plus 1/2 your social security, reaches:
Married Filing Jointly: $32,000
Single or head of household: $25,000
Married Filing Separately: 0
To see the Social Security Benefits Calculation Worksheet in Turbo Tax Online version you would have to save your return with all the worksheets to your computer. Or if you are using the Desktop CD/Download Software you can switch to Forms Mode (click Forms in the upper right) and click on SS in the list on the right side.